Article
Neurosciences
Yiting Wu, Tingwei Song, Qian Xu
Summary: Expansions of short tandem repeats (STRs) are associated with over 50 diseases, particularly neurodegenerative diseases. Several potential molecular mechanisms, including transcriptional silencing, R-LOOP formation, sequestration of RNA-binding proteins, gain-of-function proteins, and repeat-associated non-AUG translation, contribute to STR expansion disorders. R-LOOP, a three-stranded nucleic acid structure formed during transcription, plays a crucial role in inducing DNA damage and genome instability. This review provides a comprehensive discussion on the recent advancements in understanding R-LOOP and its genetic destabilizing effects in neurodegenerative diseases, offering potential targets for drug design and therapeutic advancements.
MOLECULAR NEUROBIOLOGY
(2023)
Article
Immunology
Suthirote Meesawat, Saradee Warit, Yuzuru Hamada, Suchinda Malaivijitnond
Summary: We identified tuberculosis in 1,836 macaques from various macaque populations in Thailand. Throat swab specimens were found to be the best sample medium for detecting Mycobacterium tuberculosis complex (MTBC) infections. The prevalence of MTBC was higher in rhesus macaques compared to the common and Burmese long-tailed macaques, and a higher percentage of adults were infected compared to subadults and juveniles. Bidirectional zoonotic transmission should be considered a possible public health concern.
EMERGING INFECTIOUS DISEASES
(2023)
Article
Biophysics
Olivier Tytgat, Maarten Fauvart, Tim Stakenborg, Dieter Deforce, Filip Van Nieuwerburgh
Summary: The demand for forensic DNA profiling is increasing, leading to challenges in decentralized workflow due to the need for bulky equipment. Researchers developed a novel hybridization-based STR genotyping method using STRide probes, showing high sensitivity and potential for on-site forensic DNA fingerprinting.
BIOSENSORS & BIOELECTRONICS
(2021)
Article
Cell Biology
Worapong Singchat, Syed Farhan Ahmad, Kitipong Jaisamut, Thitipong Panthum, Nattakan Ariyaraphong, Ekaphan Kraichak, Narongrit Muangmai, Prateep Duengkae, Sunchai Payungporn, Suchinda Malaivijitnond, Kornsorn Srikulnath
Summary: This study investigated the genetic diversity in the centromeric region of long-tailed and rhesus macaques, revealing diverse subfamilies and interspecific variability. The study also found admixture patterns and high level polymorphisms within populations.
Article
Multidisciplinary Sciences
Readman Chiu, Indhu-Shree Rajan-Babu, Inanc Birol, Jan M. Friedman
Summary: This study explores how the long-range sequence information of barcode linked-read sequencing (BLRS) can improve the detection of STR expansions. A novel algorithm using BLRS barcodes for distance estimation is devised and evaluated for STR genotyping. The utility of barcode and phasing information is validated through simulated and experimental data, showing improved STR genotypes compared to standard short-read sequencing.
SCIENTIFIC REPORTS
(2022)
Article
Biochemistry & Molecular Biology
Yujie Huang, Cong Liu, Chao Xiao, Xiaoying Chen, Xueli Han, Shaohua Yi, Daixin Huang
Summary: This study investigated the mutation rates of 28 autosomal STRs in the Chinese Han population, revealing relationships between STR mutation rates and factors such as population, sex, age, allele length, and heterozygosity. The results showed a higher frequency of paternal mutations compared to maternal mutations, an increase in mutation rate with paternal age, a bias towards contraction mutations for long alleles, and expansion mutations for short alleles, with no overall bias in mutation direction. Additionally, loci with higher expected heterozygosity tended to have higher mutation rates, providing valuable information for further research on STR mutations in forensic genetics.
MOLECULAR BIOLOGY REPORTS
(2021)
Article
Behavioral Sciences
Balazs Knakker, Vilmos Olah, Attila Trunk, Balazs Lendvai, Gyorgy Levay, Istvan Hernadi
Summary: The study found that the acetylcholinesterase inhibitor donepezil partially rescued the scopolamine-induced impairments of visual working memory (VWM) performance, while scopolamine-induced impairments of VWM maintenance are delay-dependent, especially affecting the time range of 15 to 33 seconds.
BEHAVIOURAL BRAIN RESEARCH
(2021)
Review
Medicine, General & Internal
Akshunna Keerti, Sudhir Ninave
Summary: Short tandem repeat (STR) markers play an important role in forensic DNA typing, allowing for tracking of missing individuals, verification of family connections, and potential linking of suspects to crime scenes. With increasing understanding of non-coding STRs, the probability of discovering meaningful connections is rising.
CUREUS JOURNAL OF MEDICAL SCIENCE
(2022)
Editorial Material
Multidisciplinary Sciences
Masanori Matsuzaki, Teppei Ebina
Summary: In June 2021, two papers utilized two-photon or one-photon microscopes to study the motor cortex in macaque monkeys over several months, successfully decoding the direction of natural arm reaching from population activity.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Annette B. Vogel, Isis Kanevsky, Ye Che, Kena A. Swanson, Alexander Muik, Mathias Vormehr, Lena M. Kranz, Kerstin C. Walzer, Stephanie Hein, Alptekin Gueler, Jakob Loschko, Mohan S. Maddur, Ayuko Ota-Setlik, Kristin Tompkins, Journey Cole, Bonny G. Lui, Thomas Ziegenhals, Arianne Plaschke, David Eisel, Sarah C. Dany, Stephanie Fesser, Stephanie Erbar, Ferdia Bates, Diana Schneider, Bernadette Jesionek, Bianca Saenger, Ann-Kathrin Wallisch, Yvonne Feuchter, Hanna Junginger, Stefanie A. Krumm, Andre P. Heinen, Petra Adams-Quack, Julia Schlereth, Stefan Schille, Christoph Kroener, Ramon de la Caridad Guimil Garcia, Thomas Hiller, Leyla Fischer, Rani S. Sellers, Shambhunath Choudhary, Olga Gonzalez, Fulvia Vascotto, Matthew R. Gutman, Jane A. Fontenot, Shannan Hall-Ursone, Kathleen Brasky, Matthew C. Griffor, Seungil Han, Andreas A. H. Su, Joshua A. Lees, Nicole L. Nedoma, Ellene H. Mashalidis, Parag Sahasrabudhe, Charles Y. Tan, Danka Pavliakova, Guy Singh, Camila Fontes-Garfias, Michael Pride, Ingrid L. Scully, Tara Ciolino, Jennifer Obregon, Michal Gazi, Ricardo Carrion, Kendra J. Alfson, Warren Kalina, Deepak Kaushal, Pei-Yong Shi, Thorsten Klamp, Corinna Rosenbaum, Andreas N. Kuhn, Ozlem Tureci, Philip R. Dormitzer, Kathrin U. Jansen, Ugur Sahin
Summary: The two vaccine candidates, BNT162b1 and BNT162b2, developed contain modified messenger RNA encoding immunogens derived from the spike glycoprotein of SARS-CoV-2. They have shown promising immune responses in mice and rhesus macaques, with ongoing phase I trials in Germany and the USA and a global phase II/III trial for BNT162b2.
Article
Biochemistry & Molecular Biology
Malika Aid, Michaela Sciacca, Katherine McMahan, David Hope, Jinyan Liu, Catherine Jacob-Dolan, Olivia Powers, Julia Barrett, Cindy Wu, Audrey Mutoni, Tetyana Murdza, Hannah Richter, Jason Velasco, Elyse Teow, Mona Boursiquot, Anthony Cook, Tatyana Orekov, Melissa Hamilton, Laurent Pessaint, Alaina Ryan, Tammy Hayes, Amanda J. Martinot, Michael S. Seaman, Mark G. Lewis, Hanne Andersen, Dan H. Barouch
Summary: The study investigates the immune responses and skin lesions caused by mpox virus in rhesus macaques infected through different routes. Transcriptomic analysis reveals insights into the pathogenesis and immunity of mpox. The macaque model shows potential for evaluating mpox vaccines and therapeutics.
Article
Cell Biology
Wan-Ting He, Meng Yuan, Sean Callaghan, Rami Musharrafieh, Ge Song, Murillo Silva, Nathan Beutler, Wen-Hsin Lee, Peter Yong, Jonathan L. Torres, Mariane Melo, Panpan Zhou, Fangzhu Zhao, Xueyong Zhu, Linghang Peng, Deli Huang, Fabio Anzanello, James Ricketts, Mara Parren, Elijah Garcia, Melissa Ferguson, William Rinaldi, Stephen A. Rawlings, David Nemazee, Davey M. Smith, Bryan Briney, Yana Safonova, Thomas F. Rogers, Jennifer M. Dan, Zeli Zhang, Daniela Weiskopf, Alessandro Sette, Shane Crotty, Darrell J. Irvine, Andrew B. Ward, Ian A. Wilson, Dennis R. Burton, Raiees Andrabi
Summary: Immunization of macaques with SARS-CoV-2 spike protein generated potent cross-neutralizing antibody responses, effective against both SARS-CoV-2 and SARS-CoV-1, as well as most SARS-CoV-2 variants.
SCIENCE TRANSLATIONAL MEDICINE
(2022)
Article
Biochemical Research Methods
Irena Zupanic Pajnic, Carlo Previdere, Tomaz Zupanc, Martina Zanon, Paolo Fattorini
Summary: The introduction of PCR-MPS technologies has changed the approach to allelic STR typing in forensics. It is found that PCR-MPS could generate isometric drop-ins (IDIs), which may mislead the operator regarding the number of contributors in a forensic evaluation. The molecular features of IDIs and duplicate tests may be useful tools for managing this new class of artifacts.
Article
Chemistry, Analytical
Olivier Tytgat, Sonja Skevin, Maarten Fauvart, Tim Stakenborg, Dieter Deforce, Filip Van Nieuwerburgh
Summary: A hybridization-based genotyping assay called QueSTR probes was developed for miniaturized lab-on-a-chip STR profiling. The QueSTR probes rely on the recognition and cleavage of an RNA:DNA duplex to achieve genotyping. The study demonstrated that the QueSTR probes have high accuracy in genotyping three core loci.
SENSORS AND ACTUATORS B-CHEMICAL
(2022)
Article
Biochemistry & Molecular Biology
Ala Moshiri, Fang Fang, Pei Zhuang, Haoliang Huang, Xue Feng, Liang Li, Roopa Dalal, Yang Hu
Summary: Researchers attempted to replicate the mouse glaucoma model in rhesus macaque monkeys and found that it successfully recapitulated the severe degeneration seen in acute human glaucoma. However, the monkeys showed dynamic changes in intraocular pressure, indicating the need for further optimization.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Agriculture, Multidisciplinary
Wei Yuan-hang, Zhao Xi-yu, Shen Xiao-xu, Ye Lin, Zhang Yao, Wang Yan, Li Di-yan, Zhu Qing, Yin Hua-dong
Summary: This study identified circEDC3 as a conservative circular RNA that can inhibit chicken skeletal muscle satellite cells (SMSCs) proliferation and differentiation. They also found that circEDC3 may have protein-coding potential.
JOURNAL OF INTEGRATIVE AGRICULTURE
(2022)
Correction
Biotechnology & Applied Microbiology
Feng Li, Chengdong Wang, Zhongxian Xu, Mingzhou Li, Linhua Deng, Ming Wei, Hemin Zhang, Kai Wu, Ruihong Ning, Diyan Li, Mingyao Yang, Mingwang Zhang, Qingyong Ni, Bo Zeng, Desheng Li, Ying Li
BIOMED RESEARCH INTERNATIONAL
(2022)
Article
Microbiology
Felix Kwame Amevor, Zhifu Cui, Xiaxia Du, Jing Feng, Gang Shu, Zifan Ning, Dan Xu, Xun Deng, Weizhen Song, Youhao Wu, Xueqing Cao, Shuo Wei, Juan He, Fanli Kong, Xiaohui Du, Yaofu Tian, Benjamin Karikari, Diyan Li, Yan Wang, Yao Zhang, Qing Zhu, Xiaoling Zhao
Summary: This study investigates the synergistic effects of quercetin and vitamin E on the composition and function of cecal microbiota, as well as the microbial metabolic profile in aged breeder hens. The results show that quercetin and vitamin E can alter the cecal microbial composition and metabolite profile, laying a foundation for chicken improvement programs.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Qingyong Ni, Shasha Dong, Bolin Xing, Bo Zeng, Fanli Kong, Huailiang Xu, Yongfang Yao, Diyan Li, Mingwang Zhang, Xiaolan Fan, Deying Yang, Mingyao Yang, Meng Xie
Summary: The study compared the fecal and oral microbiome of Bengal slow lorises under long-term and short-term captivity, revealing a higher abundance of pathogenic genera in the microbiomes of long-term captive lorises. Meanwhile, specific bacterial taxa associated with intestinal balance were more enriched in the short-term captive group.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Hua Kui, Bo Ran, Maosen Yang, Xin Shi, Yingyu Luo, Yujie Wang, Tao Wang, Diyan Li, Surong Shuai, Mingzhou Li
Summary: Chickens are important sources of protein for human diet and are used in biomedical research. The skeletal muscles of chickens have diverse origins, shapes, metabolic features, and physical functions, making increasing meat production a key goal in the poultry industry. Previous gene expression studies have overlooked the differences among various types of skeletal muscles. In this study, the researchers sequenced 58 samples from 10 different skeletal muscles of White Plymouth Rock chickens and generated a comprehensive transcriptional map, providing valuable information on muscle fiber characteristics.
Article
Biochemistry & Molecular Biology
Xiaoqin Xu, Bin Wang, Caiquan Zhou, Hualin Yang, Xue Zhong, Wanhong Li, Li Chen, Yi Jian, Long Zhang
Summary: Through next-generation sequencing, we developed and characterized markers for seven microsatellite loci of the Chinese monal. These markers exhibited moderate to high levels of polymorphism and can be used for assessing genetic backgrounds, designing conservation plans, and conducting breeding management and other related studies.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Agriculture, Dairy & Animal Science
Maosen Yang, Dong Leng, Bo Zeng, Tao Wang, Zhongxian Xu, Diyan Li
Summary: 6mA is widely present in the chicken genome and inhibits gene expression in promoter regions. It may play a role in embryonic chicken development and muscle development by regulating gene expression. These findings provide new insights into the distribution and function of 6mA modification in higher organisms.
Article
Biochemistry & Molecular Biology
Pengliang Liu, Diyan Li, Jiaman Zhang, Mengnan He, Dengfeng Gao, Yujie Wang, Yu Lin, Dengke Pan, Penghao Li, Tao Wang, Jing Li, Fanli Kong, Bo Zeng, Lu Lu, Jideng Ma, Keren Long, Guisen Li, Qianzi Tang, Long Jin, Mingzhou Li
Summary: This study elucidates the dynamics of 3D genome architecture in human adipose tissues (ATs) and the differences compared to mammalian models. The researchers found evolutionarily conserved and human-specific chromatin conformations in ATs, with human-specific conformations enriched for human-specific sequence and less conserved transcription factor binding motifs. Genes associated with conserved chromatin organization exhibit higher transcriptional conservation, while those involved in the evolutionary dynamics of chromatin organization have lower transcriptional conservation. Additionally, human-specific chromatin organization is enriched for genes involved in energy metabolism and the maintenance of metabolic homeostasis, while evolutionarily conserved chromatin organization is enriched for genes related to basic physiological functions, health, and genetic variations.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
Long Jin, Danyang Wang, Jiaman Zhang, Pengliang Liu, Yujie Wang, Yu Lin, Can Liu, Ziyin Han, Keren Long, Diyan Li, Yu Jiang, Guisen Li, Yu Zhang, Jingyi Bai, Xiaokai Li, Jing Li, Lu Lu, Fanli Kong, Xun Wang, Hua Li, Zhiqing Huang, Jideng Ma, Xiaolan Fan, Linyuan Shen, Li Zhu, Yanzhi Jiang, Guoqing Tang, Bin Feng, Bo Zeng, Liangpeng Ge, Xuewei Li, Qianzi Tang, Zhihua Zhang, Mingzhou Li
Summary: Using a pig model, the study investigates how chromatin architecture in adipose tissue is regulated in relation to obesity. Analysis of the data reveals similarities and differences in chromatin architecture between humans and pigs, providing valuable insights into the regulation of obesity-related genes.
NATURE COMMUNICATIONS
(2023)
Article
Microbiology
Junsong Zhao, Yongfang Yao, Mengmeng Dong, Hongtao Xiao, Ying Xiong, Shengzhi Yang, Diyan Li, Meng Xie, Qingyong Ni, Mingwang Zhang, Huailiang Xu
Summary: Animal gut microbiota plays a crucial role in host adaptation to different altitude environments. However, little is known about the mechanism of animal gut microbiota in adapting to high altitudes. This study analyzed the response of gut microbiota in wild macaques, humans, and dogs to diet and altitude environments, and found that high altitude environments drive the convergence of gut microbiota among species, possibly due to microbial transmission mediated by human activities.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Genetics & Heredity
Bo Ran, Wei Zhu, Xiaoling Zhao, Linxiang Li, Zhixin Yi, Miao Li, Tao Wang, Diyan Li
Summary: This study analyzed the genetic structure and evolutionary relationships of the Mountainous Meihua chicken. It found that the chicken has high genetic diversity and good breeding potential. It also showed a moderate degree of differentiation from other chicken breeds and no evidence of past population expansions. The study identified four unique maternal lineages in the Mountainous Meihua chicken.
Article
Genetics & Heredity
Hao Li, Pu Zhang, Diyan Li, Binlong Chen, Jing Li, Tao Wang
Summary: Chickens can absorb and store plant miRNAs in various tissues and organs. The plant miRNAs detected in embryos may be involved in the development of chicken embryos.
Article
Biotechnology & Applied Microbiology
Junsong Zhao, Yongfang Yao, Diyan Li, Wei Zhu, Hongtao Xiao, Meng Xie, Ying Xiong, Jiayun Wu, Qingyong Ni, Mingwang Zhang, Huailiang Xu
Summary: This study investigated the role of gut microbiota in the adaptation of rhesus macaques to high-altitude environments. The results showed that gut microbiota enriched in high-altitude populations have a stronger potential for energy synthesis and the degradation of exogenous toxins. This suggests an important energy compensatory role of gut microbiota in the adaptation to high-altitude environments.
NPJ BIOFILMS AND MICROBIOMES
(2023)
Article
Agriculture, Dairy & Animal Science
Xin Shi, Dejun Zeng, Guijun Zhao, Chenglu Zhang, Xiaolan Feng, Chengli Zheng, Diyan Li, Ming Zhang, Hang Jie
Summary: This study found that muskrat musk extracted from three-year-old muskrats is a relatively good substitute for white musk. It also suggests that the processes of amino acid biosynthesis and metabolism, steroid hormone biosynthesis, and fatty acid biosynthesis are beneficial to the secretion of muskrat musk.
Article
Multidisciplinary Sciences
Pengliang Liu, Diyan Li, Jiaman Zhang, Mengnan He, Yan Li, Rui Liu, Mingzhou Li
Summary: The storage of lipids as energy in adipose tissue is conserved, but there are substantial differences in the physiological activities of adipose tissues among species. This study characterized the transcriptional and lipidomic profiles of subcutaneous and visceral adipose tissues across 15 vertebrate species, spanning more than 300 million years of evolution. The data revealed greater variation in AT transcriptome and lipidome among species than within the same species, providing a resource for future studies on functional differences among adipose tissues in vertebrate species.
